If you want to do it yourself, it depends on how your book is set up. Do you number notes straight through (moderately straightforward to script), or by section (much less straightforward to script)? Do you use distinct styles for your note markers in the text and your note numbers in the note itself?

Another option might be to export to IDML and renumber in the XML, then reimport; it really depends on where you're comfortable automating (InDesign via script or XML via text editor).